[phenixbb] Unexpected Occupancy refiniement for ligands...

Pavel Afonine pafonine at lbl.gov
Sat Aug 13 10:38:35 PDT 2011


Hi Yuri,

yes, Ed is perfectly right - you don't want to refine occupancies of 
water at this resolution (1.5A).

Regarding the ligand: just make sure the occupancies of ligand atoms are 
all equal to each other and less than 1 (say 0.9) in your input PDB 
file. The rest will be taken care of automatically.

Pavel.

On 8/13/11 8:30 AM, Yuri wrote:
> Hey,
> So I am finishing up a model at 1.5 A and I tried to refine my ligands 
> (3) and waters (468) in addition to altloc residues.
> The residues refine as expected e.g OccA + OccB = 1.0 and all atoms in 
> A have OccA  and all the atoms in B have OccB.
> My ligands on the other are being refined as the following:
>
> HETATM 6867  C1  MLA L   3      32.357 -28.612   7.978  0.93 
> 23.77      C    C
>
> HETATM 6868  O1A MLA L   3      31.209 -28.949   7.502  0.85 
> 24.79      C    O
>
> HETATM 6869  O1B MLA L   3      32.454 -28.160   9.141  0.70 
> 22.70      C    O
>
> HETATM 6870  C2  MLA L   3      33.553 -28.727   7.095  1.00 
> 25.46      C    C
>
> HETATM 6871  C3  MLA L   3      34.774 -28.070   7.627  0.92 
> 28.45      C    C
>
> HETATM 6872  O3A MLA L   3      34.830 -27.664   8.808  1.00 
> 30.15      C    O
>
> HETATM 6873  O3B MLA L   3      35.775 -27.948   6.840  1.00 
> 30.23      C    O
>
> HETATM 6874 HC21 MLA L   3      33.321 -28.281   6.139  1.00 
> 30.56      C    H
>
> HETATM 6875 HC22 MLA L   3      33.760 -29.776   6.943  1.00 
> 30.56      C    H
>
> Each atom is getting an individual occupancy assigned, which 
> physically is impossible :)
> Any light?
> Could it be my selection syntax?
>
> Corrigendum: I think I sent a bug email last night about an error when 
> writing mtz files in refinement. It was an accident. My naming 
> convention was bad, thats why it crashed. Sorry
>



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